Display images demo
1 Setup
library(magrittr)
library(tidyverse)
library(glue)
library(arrow)batch <- params$batch
futile.logger::flog.info(glue("Batch = {batch}"))INFO [2021-05-13 12:28:31] Batch = 2020_11_04_CPJUMP1data_path <- params$data_path
git_commit_hash <- system(glue::glue("cd {data_path}; git rev-parse HEAD; cd .."), intern = TRUE)
print(glue::glue("Git commit of {data_path} = {git_commit_hash}"))Git commit of ../../pilot-cpjump1-data = e3b9f1beab59eef829cb6c99a493cf2940da757cgit_remote <- system(glue::glue("cd {data_path}; git remote -v; cd .."), intern = TRUE)
print(glue::glue("Git remote of {data_path} = {git_remote}"))Git remote of ../../pilot-cpjump1-data = origin git@github.com:jump-cellpainting/pilot-cpjump1-data.git (fetch)
Git remote of ../../pilot-cpjump1-data = origin git@github.com:jump-cellpainting/pilot-cpjump1-data.git (push)2 Display images
display_images <- function(query, lut, n_samples = 2) {
for (i in seq(nrow(query))) {
# get i'th query
query_i <- slice(query, i)
# get corresponding lookup row
lut_query <-
inner_join(lut, query_i)
# inner_join(lut, query_i, by = intersect(names(lut), names(query)))
# get tag for query
query_tag <- paste0(query_i, collapse = "__")
cat('\n\n## `', query_tag, '`\n\n')
# number of replicates to display
# NOTE: This can have unexpected output because the rows of `lut_query` may
# not really be replicates. E.g. if we specify only `Metadata_broad_sample`
# in a compound experiment that has multiple doses, `lut_query` will have
# all wells of `Metadata_broad_sample` at all dose points.
# TODO: Figure out how to handle this.
n_samples <- min(n_samples, nrow(lut_query))
for (j in seq(n_samples)) {
lut_query_j <- slice(lut_query, j)
lut_query_tag <- paste0(lut_query_j, collapse = "__")
Metadata_thumbnail_path_j <-
lut_query_j$Metadata_thumbnail_path
image_code = glue("\n\n\n\n")
cat(image_code)
cat(
lut_query_j %>%
select(-Metadata_thumbnail_path) %>%
mutate(across(everything(), as.character)) %>%
pivot_longer(everything()) %>%
format_tsv() %>%
str_replace_all("\n", "\n\n")
)
}
}
}lut_files <-
glue("{data_path}/visualize/{batch}/{batch}_.*_lut.csv")lut <-
list.files(dirname(lut_files), full.names = T, pattern = basename(lut_files)) %>%
map_df(read_csv, col_types = cols()) %>%
mutate(Metadata_thumbnail_path =
file.path(data_path, Metadata_thumbnail_path))experiment <-
data.frame(
Metadata_experiment_condition = "Standard",
Metadata_experiment_type = "Compound",
Metadata_cell_line = "U2OS",
Metadata_timepoint = 24
)
query <- tribble(
~ Metadata_broad_sample,
"BRD-K36660044-001-24-2",
"BRD-K67637637-003-11-8",
"BRD-K24616672-003-20-1",
"BRD-K61688984-001-02-9",
"BRD-K93632104-001-17-2"
)
query <- bind_cols(experiment, query)
display_images(query, lut)Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.1 Standard__Compound__U2OS__24__BRD-K36660044-001-24-2
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116995
Metadata_Well F17
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 6
Metadata_Col 17
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K36660044-001-24-2
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116995
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.1163
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HDAC6
Metadata_pert_iname bufexamac
Metadata_pubchem_cid 2466
Metadata_InChIKey MXJWRABVEGLYDG-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r06c17
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117024
Metadata_Well F17
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 6
Metadata_Col 17
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K36660044-001-24-2
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117024
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 2
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.1163
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HDAC6
Metadata_pert_iname bufexamac
Metadata_pubchem_cid 2466
Metadata_InChIKey MXJWRABVEGLYDG-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r06c17
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.2 Standard__Compound__U2OS__24__BRD-K67637637-003-11-8
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117024
Metadata_Well M03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 13
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K67637637-003-11-8
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117024
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 2
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.8694
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target S100B
Metadata_pert_iname olopatadine
Metadata_pubchem_cid 25271818
Metadata_InChIKey JBIMVDZLSHOPLA-LSCVHKIXSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r13c03
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117025
Metadata_Well M03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 13
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K67637637-003-11-8
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117025
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 3
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.8694
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target S100B
Metadata_pert_iname olopatadine
Metadata_pubchem_cid 25271818
Metadata_InChIKey JBIMVDZLSHOPLA-LSCVHKIXSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r13c03
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.3 Standard__Compound__U2OS__24__BRD-K24616672-003-20-1
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116995
Metadata_Well P21
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 16
Metadata_Col 21
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K24616672-003-20-1
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116995
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.3639
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HTR3A
Metadata_pert_iname procaine
Metadata_pubchem_cid 4914
Metadata_InChIKey MFDFERRIHVXMIY-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r16c21
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117024
Metadata_Well P21
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 16
Metadata_Col 21
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K24616672-003-20-1
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117024
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 2
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.3639
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HTR3A
Metadata_pert_iname procaine
Metadata_pubchem_cid 4914
Metadata_InChIKey MFDFERRIHVXMIY-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r16c21
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.4 Standard__Compound__U2OS__24__BRD-K61688984-001-02-9
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116995
Metadata_Well H03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 8
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K61688984-001-02-9
Metadata_genes NA
Metadata_pert_type control
Metadata_control_type poscon_cp
Metadata_Assay_Plate_Barcode BR00116995
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.812
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HDAC3
Metadata_pert_iname RGFP966
Metadata_pubchem_cid 56650312
Metadata_InChIKey BLVQHYHDYFTPDV-VCABWLAWSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r08c03
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117024
Metadata_Well H03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 8
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K61688984-001-02-9
Metadata_genes NA
Metadata_pert_type control
Metadata_control_type poscon_cp
Metadata_Assay_Plate_Barcode BR00117024
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 2
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 1.812
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target HDAC3
Metadata_pert_iname RGFP966
Metadata_pubchem_cid 56650312
Metadata_InChIKey BLVQHYHDYFTPDV-VCABWLAWSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r08c03
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.5 Standard__Compound__U2OS__24__BRD-K93632104-001-17-2
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117024
Metadata_Well O03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 15
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K93632104-001-17-2
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117024
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 2
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 0.6906
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target AKR1C1
Metadata_pert_iname salicylic-acid|sodium-salicylate
Metadata_pubchem_cid 118212070
Metadata_InChIKey YGSDEFSMJLZEOE-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r15c03
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117025
Metadata_Well O03
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 15
Metadata_Col 3
Metadata_plate_map_name C-7210-01-CMP-013
Metadata_broad_sample BRD-K93632104-001-17-2
Metadata_genes NA
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117025
Metadata_Plate_Map_Name C-7210-01-CMP-013
Metadata_cell_line U2OS
Metadata_timepoint 24
Metadata_experiment_type Compound
Metadata_experiment_condition Standard
Metadata_replicate_id 3
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml 0.6906
Metadata_mmoles_per_liter 5
Metadata_solvent DMSO
Metadata_target AKR1C1
Metadata_pert_iname salicylic-acid|sodium-salicylate
Metadata_pubchem_cid 118212070
Metadata_InChIKey YGSDEFSMJLZEOE-UHFFFAOYSA-N
Metadata_gene NA
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r15c03
Metadata_cachedir image_cache
Metadata_montagedir montage
experiment <-
data.frame(
Metadata_experiment_condition = "Standard",
Metadata_experiment_type = "CRISPR",
Metadata_cell_line = "U2OS",
Metadata_timepoint = 144
)
query <- tribble(
~ Metadata_broad_sample,
"BRDN0001146959",
"BRDN0000585461",
"BRDN0001483257",
"BRDN0001480092",
"BRDN0001054815"
)
query <- bind_cols(experiment, query)
display_images(query, lut)Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.6 Standard__CRISPR__U2OS__144__BRDN0001146959
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116996
Metadata_Well C08
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 3
Metadata_Col 8
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001146959
Metadata_genes CSF1R
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116996
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 4
Metadata_negcon_control_type NA
Metadata_target_sequence ACGCTACCTTCCAAAACACG
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target CSF1R
Metadata_pert_iname BRDN0001146959
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene CSF1R
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r03c08
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116997
Metadata_Well C08
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 3
Metadata_Col 8
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001146959
Metadata_genes CSF1R
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116997
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence ACGCTACCTTCCAAAACACG
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target CSF1R
Metadata_pert_iname BRDN0001146959
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene CSF1R
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r03c08
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.7 Standard__CRISPR__U2OS__144__BRDN0000585461
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116996
Metadata_Well M23
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 13
Metadata_Col 23
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0000585461
Metadata_genes HCK
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116996
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 4
Metadata_negcon_control_type NA
Metadata_target_sequence CCGTGCGAGACTACGACCCT
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HCK
Metadata_pert_iname BRDN0000585461
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HCK
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r13c23
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116997
Metadata_Well M23
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 13
Metadata_Col 23
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0000585461
Metadata_genes HCK
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116997
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence CCGTGCGAGACTACGACCCT
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HCK
Metadata_pert_iname BRDN0000585461
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HCK
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r13c23
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.8 Standard__CRISPR__U2OS__144__BRDN0001483257
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116996
Metadata_Well I04
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 9
Metadata_Col 4
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001483257
Metadata_genes HSP90AA1
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00116996
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 4
Metadata_negcon_control_type NA
Metadata_target_sequence GATCAAAAGGAGCACGTCGT
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HSP90AA1
Metadata_pert_iname BRDN0001483257
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HSP90AA1
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r09c04
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116997
Metadata_Well I04
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 9
Metadata_Col 4
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001483257
Metadata_genes HSP90AA1
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00116997
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence GATCAAAAGGAGCACGTCGT
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HSP90AA1
Metadata_pert_iname BRDN0001483257
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HSP90AA1
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r09c04
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.9 Standard__CRISPR__U2OS__144__BRDN0001480092
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116996
Metadata_Well F12
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 6
Metadata_Col 12
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001480092
Metadata_genes PARP3
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116996
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 4
Metadata_negcon_control_type NA
Metadata_target_sequence AGCAAGCAACAGATTGCACG
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target PARP3
Metadata_pert_iname BRDN0001480092
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene PARP3
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r06c12
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116997
Metadata_Well F12
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 6
Metadata_Col 12
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001480092
Metadata_genes PARP3
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00116997
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence AGCAAGCAACAGATTGCACG
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target PARP3
Metadata_pert_iname BRDN0001480092
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene PARP3
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r06c12
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.10 Standard__CRISPR__U2OS__144__BRDN0001054815
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116996
Metadata_Well D21
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 4
Metadata_Col 21
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001054815
Metadata_genes KRAS
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00116996
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 4
Metadata_negcon_control_type NA
Metadata_target_sequence CAGTACATGAGGACTGGGGA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target KRAS
Metadata_pert_iname BRDN0001054815
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene KRAS
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r04c21
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00116997
Metadata_Well D21
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 4
Metadata_Col 21
Metadata_plate_map_name DXH.92.93.94.95.A
Metadata_broad_sample BRDN0001054815
Metadata_genes KRAS
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00116997
Metadata_Plate_Map_Name DXH.92.93.94.95.A
Metadata_cell_line U2OS
Metadata_timepoint 144
Metadata_experiment_type CRISPR
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence CAGTACATGAGGACTGGGGA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target KRAS
Metadata_pert_iname BRDN0001054815
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene KRAS
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r04c21
Metadata_cachedir image_cache
Metadata_montagedir montage
experiment <-
data.frame(
Metadata_experiment_condition = "Standard",
Metadata_experiment_type = "ORF",
Metadata_cell_line = "U2OS",
Metadata_timepoint = 48
)
query <- tribble(
~ Metadata_broad_sample,
"ccsbBroad304_14597",
"ccsbBroad304_00733",
"ccsbBroad304_06412",
"ccsbBroad304_07535",
"ccsbBroad304_16173"
)
query <- bind_cols(experiment, query)
display_images(query, lut)Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.11 Standard__ORF__U2OS__48__ccsbBroad304_14597
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well D14
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 4
Metadata_Col 14
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_14597
Metadata_genes CSF1R
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target CSF1R
Metadata_pert_iname ccsbBroad304_14597
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene CSF1R
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r04c14
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well J07
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 10
Metadata_Col 7
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_14597
Metadata_genes CSF1R
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target CSF1R
Metadata_pert_iname ccsbBroad304_14597
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene CSF1R
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r10c07
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.12 Standard__ORF__U2OS__48__ccsbBroad304_00733
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well O01
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 15
Metadata_Col 1
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_00733
Metadata_genes HCK
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HCK
Metadata_pert_iname ccsbBroad304_00733
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HCK
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r15c01
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well O20
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 15
Metadata_Col 20
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_00733
Metadata_genes HCK
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HCK
Metadata_pert_iname ccsbBroad304_00733
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HCK
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r15c20
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.13 Standard__ORF__U2OS__48__ccsbBroad304_06412
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well C14
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 3
Metadata_Col 14
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_06412
Metadata_genes HSP90AA1
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HSP90AA1
Metadata_pert_iname ccsbBroad304_06412
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HSP90AA1
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r03c14
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well E13
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 5
Metadata_Col 13
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_06412
Metadata_genes HSP90AA1
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target HSP90AA1
Metadata_pert_iname ccsbBroad304_06412
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene HSP90AA1
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r05c13
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.14 Standard__ORF__U2OS__48__ccsbBroad304_07535
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well H21
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 8
Metadata_Col 21
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_07535
Metadata_genes PARP3
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target PARP3
Metadata_pert_iname ccsbBroad304_07535
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene PARP3
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r08c21
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well J20
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 10
Metadata_Col 20
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_07535
Metadata_genes PARP3
Metadata_pert_type trt
Metadata_control_type NA
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target PARP3
Metadata_pert_iname ccsbBroad304_07535
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene PARP3
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r10c20
Metadata_cachedir image_cache
Metadata_montagedir montage
Joining, by = c("Metadata_broad_sample", "Metadata_cell_line", "Metadata_timepoint", "Metadata_experiment_type", "Metadata_experiment_condition")2.15 Standard__ORF__U2OS__48__ccsbBroad304_16173
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well D17
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 4
Metadata_Col 17
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_16173
Metadata_genes KRAS
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target KRAS
Metadata_pert_iname ccsbBroad304_16173
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene KRAS
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r04c17
Metadata_cachedir image_cache
Metadata_montagedir montage
name value
Metadata_Batch 2020_11_04_CPJUMP1
Metadata_Plate BR00117022
Metadata_Well F08
Metadata_Site 1
Metadata_FieldID 1
Metadata_Row 6
Metadata_Col 8
Metadata_plate_map_name DOG.30.31.32.33.A
Metadata_broad_sample ccsbBroad304_16173
Metadata_genes KRAS
Metadata_pert_type control
Metadata_control_type poscon_diverse
Metadata_Assay_Plate_Barcode BR00117022
Metadata_Plate_Map_Name DOG.30.31.32.33.A
Metadata_cell_line U2OS
Metadata_timepoint 48
Metadata_experiment_type ORF
Metadata_experiment_condition Standard
Metadata_replicate_id 1
Metadata_negcon_control_type NA
Metadata_target_sequence NA
Metadata_mg_per_ml NA
Metadata_mmoles_per_liter NA
Metadata_solvent NA
Metadata_target KRAS
Metadata_pert_iname ccsbBroad304_16173
Metadata_pubchem_cid NA
Metadata_InChIKey NA
Metadata_gene KRAS
Metadata_negcon_or_other pert
Metadata_negcon_control_type_trimmed NA
Metadata_WellCode r06c08
Metadata_cachedir image_cache
Metadata_montagedir montage